[gmx-users] restart md from the point it had stopped

[Diego Enry]

gmxcheck -f broken.trr

check this information:

Item        #frames Timestep (ps)
Step           101    10
Time           101    10
Lambda        101    10
Coords         101    10
Velocities     101  10
Forces           101  10
Box            101    10

I writing it every 1ps.
I recommend you NOT to use the LAST frame because it may be corrupted
if your simulation was terminated while writing this frame. To
continue, specify the frame just before the last one find above.

tpbconv -s broken.tpr -f broken.trr -e broken.edr -o continue.tpr -time 9

Check If you write velocities&force to the .trr file, I think you
can't get a good continuation without that information.


On 10/8/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Sarbani,
>
> Use tpbconv. You can only (properly) restart from a point where you have a
> frame with velocities (in the .trr file) and preferrably energies (.edr).
>
> Best,
>
> Tsjerk
>
>
>  On 8 Oct 2007 12:34:23 -0000, sarbani chattopadhyay
> <sarbani_c84 at rediffmail.com> wrote:
> >
> >
> >
> >
> > hi,
> >   I have been running a molecular dynamics simulation for 2
> nanoseconds.But it stopped in
> > the middle because of an internal problem.Is there any way to restart the
> simulation from
> > the point it has stopped?
> >
>        Thank all
> >
>          Sarbani
> >
> >
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
>  P: +31-30-2539931
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.